Multiple sequence alignment - TraesCS1A01G000400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G000400 chr1A 100.000 2297 0 0 1 2297 120263 122559 0 4242
1 TraesCS1A01G000400 chrUn 97.997 2297 46 0 1 2297 291535440 291537736 0 3988
2 TraesCS1A01G000400 chrUn 97.997 2297 45 1 1 2297 245706068 245708363 0 3986
3 TraesCS1A01G000400 chrUn 97.954 2297 47 0 1 2297 199874824 199877120 0 3982
4 TraesCS1A01G000400 chrUn 97.954 2297 47 0 1 2297 229310227 229307931 0 3982
5 TraesCS1A01G000400 chrUn 97.955 2298 46 1 1 2297 274341282 274338985 0 3982
6 TraesCS1A01G000400 chrUn 97.780 2297 51 0 1 2297 3845814 3843518 0 3960
7 TraesCS1A01G000400 chr1B 97.954 2297 45 1 1 2297 544593697 544595991 0 3980
8 TraesCS1A01G000400 chr1B 97.780 2297 51 0 1 2297 80730657 80728361 0 3960
9 TraesCS1A01G000400 chr1B 97.780 2297 51 0 1 2297 544623636 544625932 0 3960


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G000400 chr1A 120263 122559 2296 False 4242 4242 100.000 1 2297 1 chr1A.!!$F1 2296
1 TraesCS1A01G000400 chrUn 291535440 291537736 2296 False 3988 3988 97.997 1 2297 1 chrUn.!!$F3 2296
2 TraesCS1A01G000400 chrUn 245706068 245708363 2295 False 3986 3986 97.997 1 2297 1 chrUn.!!$F2 2296
3 TraesCS1A01G000400 chrUn 199874824 199877120 2296 False 3982 3982 97.954 1 2297 1 chrUn.!!$F1 2296
4 TraesCS1A01G000400 chrUn 229307931 229310227 2296 True 3982 3982 97.954 1 2297 1 chrUn.!!$R2 2296
5 TraesCS1A01G000400 chrUn 274338985 274341282 2297 True 3982 3982 97.955 1 2297 1 chrUn.!!$R3 2296
6 TraesCS1A01G000400 chrUn 3843518 3845814 2296 True 3960 3960 97.780 1 2297 1 chrUn.!!$R1 2296
7 TraesCS1A01G000400 chr1B 544593697 544595991 2294 False 3980 3980 97.954 1 2297 1 chr1B.!!$F1 2296
8 TraesCS1A01G000400 chr1B 80728361 80730657 2296 True 3960 3960 97.780 1 2297 1 chr1B.!!$R1 2296
9 TraesCS1A01G000400 chr1B 544623636 544625932 2296 False 3960 3960 97.780 1 2297 1 chr1B.!!$F2 2296

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
422 423 0.460284 ACCTGCCGAATCAACTAGCG 60.46 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1473 0.26023 TTCCCTTGGCTGTGGTTTCA 59.74 50.0 0.0 0.0 0.0 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.054687 ACGTGCAAATCGTTCGTCTA 57.945 45.000 0.00 0.00 38.38 2.59
117 118 3.574826 GGAGCCCATTACGAGTTCTATCT 59.425 47.826 0.00 0.00 0.00 1.98
148 149 4.263816 CCAATGATTAGAGGCATCAGGGAT 60.264 45.833 0.00 0.00 34.12 3.85
179 180 7.266400 GTCCTCGACCTATTCTCAAACTTTAT 58.734 38.462 0.00 0.00 0.00 1.40
263 264 4.219725 GGCCATTTTTGGTAAGCAGAACTA 59.780 41.667 0.00 0.00 0.00 2.24
306 307 1.678724 GGGTTACGGTGCCCAACTA 59.321 57.895 15.03 0.00 44.23 2.24
319 320 1.553308 CCAACTACGCGCTAACCTAC 58.447 55.000 5.73 0.00 0.00 3.18
422 423 0.460284 ACCTGCCGAATCAACTAGCG 60.460 55.000 0.00 0.00 0.00 4.26
423 424 0.460284 CCTGCCGAATCAACTAGCGT 60.460 55.000 0.00 0.00 0.00 5.07
469 470 3.087253 CCCACACCCGGCCATCTA 61.087 66.667 2.24 0.00 0.00 1.98
503 504 1.338136 CCCAATGAGTAGGAGGGCGT 61.338 60.000 0.00 0.00 31.81 5.68
705 706 4.545706 GATCACGCGCATCCCCCA 62.546 66.667 5.73 0.00 0.00 4.96
811 812 5.639931 GCCTCGTGAAGAGTTATCTTTTCTT 59.360 40.000 5.86 0.00 45.98 2.52
838 839 1.152567 CCTGCCAACCCTGGAAACA 60.153 57.895 0.00 0.00 46.92 2.83
1435 1436 0.809636 TAGTGACGCGCATGAATGGG 60.810 55.000 5.73 3.14 42.88 4.00
1472 1473 3.269906 ACTGTCCCTGTCTACTATCCAGT 59.730 47.826 0.00 0.00 38.91 4.00
1509 1510 2.749839 CGGGCTTGGCGGAATCAA 60.750 61.111 0.00 0.00 0.00 2.57
1619 1621 3.435671 GCGCAAGTGAAATACCACTACTT 59.564 43.478 0.30 0.00 45.82 2.24
1677 1681 0.251787 GCATGTCCCCTCCTTTTGGT 60.252 55.000 0.00 0.00 41.38 3.67
1723 1727 1.674322 CCGGGCGGAAGACATTGTT 60.674 57.895 0.00 0.00 45.40 2.83
1767 1771 5.221048 GGCGGCACATCTGTTAAAAGATAAT 60.221 40.000 7.86 0.00 35.09 1.28
1884 1888 0.739462 CGTGAAAGCGTGGCCTATCA 60.739 55.000 3.32 0.00 0.00 2.15
1900 1904 6.329986 TGGCCTATCAATCCTTTAGATCTTCA 59.670 38.462 3.32 0.00 32.47 3.02
2020 2024 3.068732 TCGGCTCTTCCTATCATTGTGAG 59.931 47.826 0.00 0.00 0.00 3.51
2107 2111 3.069872 TCGTGAGCCAGGTTAGTTTTACA 59.930 43.478 0.00 0.00 0.00 2.41
2152 2156 9.399797 TGATAGTAATTCAACCTAGTACGAGAA 57.600 33.333 4.34 0.00 0.00 2.87
2223 2227 2.813908 CGAAGCTACCGTGTGCCC 60.814 66.667 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.587066 TTCGCCCCTATACCCAAGTT 58.413 50.000 0.00 0.00 0.00 2.66
142 143 1.811266 CGAGGACGTTGCATCCCTG 60.811 63.158 1.05 0.00 36.86 4.45
143 144 1.982395 TCGAGGACGTTGCATCCCT 60.982 57.895 1.05 0.00 40.69 4.20
148 149 0.892755 AATAGGTCGAGGACGTTGCA 59.107 50.000 0.00 0.00 40.69 4.08
179 180 1.171308 GTCGCGCCATCCTACCTATA 58.829 55.000 0.00 0.00 0.00 1.31
263 264 2.203070 GGTTCATCCCGCATCGCT 60.203 61.111 0.00 0.00 0.00 4.93
306 307 1.079612 GGGTTGTAGGTTAGCGCGT 60.080 57.895 8.43 0.00 0.00 6.01
422 423 0.248215 CAGCGCCATCCATTTTCGAC 60.248 55.000 2.29 0.00 0.00 4.20
423 424 0.392327 TCAGCGCCATCCATTTTCGA 60.392 50.000 2.29 0.00 0.00 3.71
487 488 1.972660 GCCACGCCCTCCTACTCATT 61.973 60.000 0.00 0.00 0.00 2.57
631 632 1.247567 GCTTACCCATGTGCAAGTGT 58.752 50.000 0.00 0.00 0.00 3.55
705 706 5.421056 GGAAATCTTAACCCGATTCCCTTTT 59.579 40.000 0.00 0.00 31.12 2.27
793 794 9.204570 CCGTTAAGAAGAAAAGATAACTCTTCA 57.795 33.333 12.23 0.00 44.94 3.02
811 812 1.302993 GGTTGGCAGGCCGTTAAGA 60.303 57.895 5.74 0.00 39.42 2.10
838 839 1.686110 CCCTACCTCCGGCTGAACT 60.686 63.158 0.00 0.00 0.00 3.01
910 911 0.106519 CCTCCGGATTTTCATGGGCT 60.107 55.000 3.57 0.00 0.00 5.19
1107 1108 2.028190 CTCGAGCAATCCGCCGAT 59.972 61.111 0.00 0.00 44.04 4.18
1435 1436 3.259902 GGACAGTGGGAATCTCGTTAAC 58.740 50.000 0.00 0.00 0.00 2.01
1472 1473 0.260230 TTCCCTTGGCTGTGGTTTCA 59.740 50.000 0.00 0.00 0.00 2.69
1509 1510 2.529389 AGGGTCTTCTTGCCCCGT 60.529 61.111 0.00 0.00 45.95 5.28
1515 1516 2.551459 CAAGCTCAACAGGGTCTTCTTG 59.449 50.000 0.00 0.00 0.00 3.02
1677 1681 1.681076 GTAAGACCGGGCCTTGGAA 59.319 57.895 19.67 0.00 0.00 3.53
1723 1727 1.497309 CCAGCCAAACTCCCCACCTA 61.497 60.000 0.00 0.00 0.00 3.08
1767 1771 1.208052 GCTCATCTTAGGACACCTGCA 59.792 52.381 0.00 0.00 34.61 4.41
1900 1904 3.898123 TGACACCTCTAGCTTCAAACTCT 59.102 43.478 0.00 0.00 0.00 3.24
2020 2024 2.288395 CCAACACTTGGTGAATTCTGCC 60.288 50.000 7.05 9.52 45.93 4.85
2051 2055 1.338769 GCTCACGTTCCCTATTGGTGT 60.339 52.381 0.00 0.00 34.77 4.16
2084 2088 3.418684 AAAACTAACCTGGCTCACGAT 57.581 42.857 0.00 0.00 0.00 3.73
2092 2096 7.331193 GTCATCAGTAGTGTAAAACTAACCTGG 59.669 40.741 0.00 0.00 43.08 4.45
2126 2130 8.969260 TCTCGTACTAGGTTGAATTACTATCA 57.031 34.615 0.00 0.00 0.00 2.15
2152 2156 4.261572 CCAATTGTGTGAATCAACGGTTCT 60.262 41.667 4.43 0.00 0.00 3.01
2223 2227 3.085443 AGAGGCGTTCAGTCATAATCG 57.915 47.619 0.00 0.00 0.00 3.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.